Table I. Synthetic peptide sequences and relative quantifications.
| Peptide number | CST product number | Protein and peptide positions | Synthetic peptide sequence and PTMs | Mass shift (Da) | Endogenous peptide (propionylated) MH+ mass | Synthetic peptide (propionylated) MH+ mass | Relative abundance (%) |
|---|---|---|---|---|---|---|---|
| 1 | 11188 | Histone H3 1–8 | ARTKQTAR | 8.014 | 1043.596 | 1051.610 | 0.305 |
| 2 | 11189 | ARme1TKQTAR | 8.014 | 1057.612 | 1065.626 | 0.375 | |
| 3 | 11190 | Histone H3 3–8 | TKQTAR | 4.007 | 816.458 | 820.465 | 0.0326 |
| 4 | 11191 | TKme1QTAR | 4.007 | 830.474 | 834.481 | 0.178 | |
| 5 | 11192 | TKme2QTAR | 4.007 | 788.463 | 792.470 | 0.0018 | |
| 6 | 11193 | TKme3QTAR | 4.007 | 802.478 | 806.485 | 0.0019 | |
| 7 | 11194 | TphKQTAR | 4.007 | 896.424 | 900.431 | 0.0055 | |
| 8 | 11195 | Histone H3 9–17 | KSTGGKAPR | 6.014 | 1069.601 | 1075.614 | 0.571 |
| 9 | 11197 | Kme1STGGKAPR | 6.014 | 1083.616 | 1089.630 | 1.295 | |
| 10 | 11198 | Kme2STGGKAPR | 6.014 | 1041.606 | 1047.619 | 0.303 | |
| 11 | 11199 | Kme3STGGKAPR | 12.021 | 1055.621 | 1067.642 | 0.252 | |
| 12 | 11196 | KacSTGGKAPR | 6.014 | 1055.584 | 1061.598 | 0.314 | |
| 13 | 11200 | KSTGGKacAPR | 9.018 | 1055.584 | 1064.602 | 0.378 | |
| 14 | 11201 | Kme1STGGKacAPR | 6.014 | 1069.600 | 1075.614 | 1.014 | |
| 15 | 11202 | Kme2STGGKacAPR | 6.014 | 1027.589 | 1033.603 | 0.177 | |
| 16 | 11203 | Kme3STGGKacAPR | 10.021 | 1041.605 | 1051.625 | 0.156 | |
| 17 | 11204 | KacSTGGKacAPR | 6.014 | 1041.568 | 1047.582 | 0.276 | |
| 18 | 11205 | KSphTGGKAPR | 6.014 | 1149.566 | 1155.580 | 0.238 | |
| 19 | 11206 | Kme1SphTGGKAPR | 6.014 | 1163.582 | 1169.596 | 0.622 | |
| 20 | 11207 | Kme2SphTGGKAPR | 6.014 | 1121.571 | 1127.585 | 0.204 | |
| 21 | 11208 | Kme3SphTGGKAPR | 6.014 | 1135.587 | 1141.600 | 0.160 | |
| 22 | 11209 | Histone H3 18–26 | KQLATKAAR | 7.017 | 1154.690 | 1161.707 | 1.608 |
| 23 | 11211 | Kme1QLATKAAR | 7.017 | 1168.705 | 1175.723 | 1.210 | |
| 24 | 11213 | KQLATKme1AAR | 11.024 | 1168.705 | 1179.730 | 1.591 | |
| 25 | 11210 | KacQLATKAAR | 7.017 | 1140.674 | 1147.691 | 1.553 | |
| 26 | 11212 | KQLATKacAAR | 15.031 | 1140.674 | 1155.705 | 1.307 | |
| 27 | 11214 | KacQLATKacAAR | 7.017 | 1126.657 | 1133.675 | 1.711 | |
| 28 | 11215 | Histone H3 27–40 | KSAPATGGVKKPHR | 6.014 | 1657.939 | 1663.953 | 1.885 |
| 29 | 11217 | Kme1SAPATGGVKKPHR | 6.014 | 1671.955 | 1677.968 | 2.081 | |
| 30 | 11218 | Kme2SAPATGGVKKPHR | 6.014 | 1629.944 | 1635.958 | 3.201 | |
| 31 | 11219 | Kme3SAPATGGVKKPHR | 10.021 | 1643.959 | 1653.980 | 3.176 | |
| 32 | 11216 | KacSAPATGGVKKPHR | 6.014 | 1643.923 | 1649.937 | 2.305 | |
| 33 | 11220 | KSAPATGGVKme1KPHR | 9.018 | 1671.955 | 1680.972 | 1.870 | |
| 34 | 11221 | KSAPATGGVKme2KPHR | 9.018 | 1629.944 | 1638.962 | 1.678 | |
| 35 | 11222 | KSAPATGGVKme3KPHR | 9.018 | 1643.959 | 1652.977 | 1.762 | |
| 36 | 11223 | Kme1SAPATGGVKme1KPHR | 12.028 | 1685.970 | 1697.998 | 1.377 | |
| 37 | 11224 | Kme1SAPATGGVKme2KPHR | 12.028 | 1643.959 | 1655.987 | 1.377 | |
| 38 | 11225 | Kme1SAPATGGVKme3KPHR | 6.014 | 1657.975 | 1663.989 | 1.670 | |
| 39 | 11226 | Kme2SAPATGGVKme1KPHR | 15.031 | 1643.959 | 1658.990 | 2.288 | |
| 40 | 11227 | Kme2SAPATGGVKme2KPHR | 9.018 | 1601.949 | 1610.967 | 1.619 | |
| 41 | 11228 | Kme2SAPATGGVKme3KPHR | 6.014 | 1615.964 | 1621.978 | 2.119 | |
| 42 | 11229 | Kme3SAPATGGVKme1KPHR | 12.028 | 1657.975 | 1670.002 | 2.840 | |
| 43 | 11230 | Kme3SAPATGGVKme2KPHR | 9.018 | 1615.964 | 1624.982 | 1.653 | |
| 44 | 11231 | Kme3SAPATGGVKme3KPHR | 6.014 | 1629.979 | 1635.993 | 1.746 | |
| 45 | 11232 | KSphAPATGGVKKPHR | 6.014 | 1737.905 | 1743.919 | 1.647 | |
| 46 | 11233 | Kme1SphAPATGGVKKPHR | 6.014 | 1751.920 | 1757.934 | 1.438 | |
| 47 | 11234 | Kme2SphAPATGGVKKPHR | 6.014 | 1709.910 | 1715.924 | 2.894 | |
| 48 | 11235 | Kme3SphAPATGGVKKPHR | 6.014 | 1723.925 | 1729.939 | 2.222 | |
| 49 | 11242 | Histone H3 41–49 | YRPGTVALR | 7.017 | 1088.622 | 1095.639 | 0.654 |
| 50 | 11240 | Histone H3 54–63 | YQKSTELLIR | 7.017 | 1362.763 | 1369.780 | 0.217 |
| 51 | 11241 | YQKacSTELLIR | 7.017 | 1348.747 | 1355.764 | 0.512 | |
| 52 | 11236 | Histone H3 73–83 | EIAQDFKTDLR | 7.017 | 1447.743 | 1454.760 | 0.125 |
| 53 | 11237 | EIAQDFKme1TDLR | 7.017 | 1461.759 | 1468.776 | 0.069 | |
| 54 | 11238 | EIAQDFKme2TDLR | 7.017 | 1419.748 | 1426.765 | 0.548 | |
| 55 | 11239 | EIAQDFKme3TDLR | 7.017 | 1433.763 | 1440.781 | 0.668 | |
| 56 | 11243 | Histone H4 1–17 | acSGRGKGGKGLGKGGAKR | 7.017 | 1837.040 | 1844.057 | 1.227 |
| 57 | 11244 | acSGRme1GKGGKGLGKGGAKR | 7.017 | 1851.056 | 1858.073 | 1.878 | |
| 58 | 11245 | Histone H4 4–17 | GKGGKGLGKGGAKR | 7.017 | 1550.902 | 1557.919 | 1.872 |
| 59 | 11246 | GKGGKGLGKGGAKacR | 6.008 | 1536.886 | 1542.893 | 1.500 | |
| 60 | 11247 | GKGGKGLGKacGGAKR | 9.011 | 1536.886 | 1545.897 | 1.788 | |
| 61 | 11248 | GKGGKacGLGKGGAKR | 11.024 | 1536.886 | 1547.910 | 1.357 | |
| 62 | 11249 | GKacGGKGLGKGGAKR | 14.028 | 1536.886 | 1550.914 | 1.950 | |
| 63 | 11250 | GKacGGKGLGKGGAKacR | 6.008 | 1522.869 | 1528.877 | 2.011 | |
| 64 | 11251 | GKGGKacGLGKGGAKacR | 7.017 | 1522.869 | 1529.887 | 1.023 | |
| 65 | 11252 | GKGGKGLGKacGGAKacR | 9.011 | 1522.869 | 1531.881 | 1.401 | |
| 66 | 11253 | GKacGGKGLGKacGGAKR | 11.024 | 1522.869 | 1533.894 | 1.431 | |
| 67 | 11254 | GKGGKacGLGKacGGAKR | 13.025 | 1522.869 | 1535.894 | 1.633 | |
| 68 | 11255 | GKacGGKacGLGKGGAKR | 14.028 | 1522.869 | 1536.897 | 1.000 | |
| 69 | 11256 | GKGGKacGLGKacGGAKacR | 6.008 | 1508.853 | 1514.861 | 1.644 | |
| 70 | 11257 | GKacGGKGLGKacGGAKacR | 9.011 | 1508.853 | 1517.864 | 1.317 | |
| 71 | 11258 | GKacGGKacGLGKGGAKacR | 11.024 | 1508.853 | 1519.877 | 1.315 | |
| 72 | 11259 | GKacGGKacGLGKacGGAKR | 14.028 | 1508.853 | 1522.881 | 1.589 | |
| 73 | 11260 | GKacGGKacGLGKacGGAKacR | 7.017 | 1494.837 | 1501.854 | 1.399 | |
| 74 | 11261 | Histone H4 20–23 | KVLR | 7.017 | 627.419 | 634.436 | 0.946 |
| 75 | 11262 | Kme1VLR | 7.017 | 641.435 | 648.452 | 1.412 | |
| 76 | 11263 | Kme2VLR | 7.017 | 599.424 | 606.442 | 0.078 | |
| 77 | 11264 | Kme3VLR | 7.017 | 613.440 | 620.457 | 0.075 | |
| 78 | 11265 | Histone H4 68–78 | DAVTYTEHAKR | 6.014 | 1402.697 | 1408.710 | 0.411 |
| 79 | 11274 | Canonical histone H2A 4–11 | GKQGGKAR | 7.011 | 969.548 | 976.559 | 0.329 |
| 80 | 11275 | GKQGGKacAR | 7.011 | 955.532 | 962.543 | 0.123 | |
| 81 | 11276 | GKacQGGKAR | 10.015 | 955.532 | 965.546 | 0.070 | |
| 82 | 11277 | GKacQGGKacAR | 7.011 | 941.516 | 948.526 | 0.030 | |
| 83 | 11273 | Canonical histone H2A 82–88 | HLQLAIR | 7.017 | 906.552 | 913.570 | 1.338 |
| 84 | 11278 | Histone H2A.Z 1–19 | AGGKAGKDSGKAKTKAVSR | 6.014 | 2153.193 | 2159.207 | 0.720 |
| 85 | 11279 | AGGKacAGKDSGKAKTKAVSR | 6.014 | 2139.177 | 2145.190 | 0.754 | |
| 86 | 11280 | AGGKAGKacDSGKAKTKAVSR | 9.018 | 2139.177 | 2148.194 | 0.422 | |
| 87 | 11281 | AGGKAGKDSGKacAKTKAVSR | 12.021 | 2139.177 | 2151.198 | 0.616 | |
| 88 | 11282 | AGGKAGKacDSGKacAKTKAVSR | 6.014 | 2125.160 | 2131.174 | 0.338 | |
| 89 | 11283 | AGGKacAGKDSGKacAKTKAVSR | 9.018 | 2125.160 | 2134.178 | 0.944 | |
| 90 | 11284 | AGGKacAGKacDSGKAKTKAVSR | 12.021 | 2125.160 | 2137.182 | 0.756 | |
| 91 | 11285 | AGGKacAGKacDSGKacAKTKAVSR | 6.014 | 2111.144 | 2117.158 | 0.731 | |
| 92 | 11286 | Histone macroH2A 44–55 | SAKAGVIFPVGR | 6.014 | 1313.758 | 1319.772 | 0.856 |
| 93 | 11287 | Histone H2A.X 4–11 | GKTGGKAR | 7.011 | 942.537 | 949.548 | 0.235 |
93 histone peptides with various PTMs were synthesized with stable isotope (C13 and N15)-labeled amino acids (underlined in the column “Synthetic Peptide Sequence and PTMs”). me1, -2, and -3 denote mono-, di-, and tri-methylation; ph, phosphorylation; ac, acetylation. The peptide number used in Fig. 2 is shown in the first column. Cell Signaling Technology Inc. product numbers are shown in the second column. The averaged relative abundance in the last column represents the detection efficiencies of these peptides.